[gmx-users] Re: genbox problem with micelle

[Alif M Latif]

Dear GROMACS users and developers,

Thanks for the response. Just want to add.. my micelle structure, built with Packmol, consists of  10 molecules  of Span20  (C18, O6, and 3 polar H) ,  90 molecules of oleyl oleate ( C36 , O2 with no polar H). This is the 1:9 ratio of surfactant : oil determined from the experimental results. So my micelle I presume is quite big. I packed the molecules, so that the oils accumulate inside (d = 13) while the surfactant's tail (non-polar) facing to it (d = 14) and the surfactant head (polar groups) facing outside the sphere (d = 19). I've done 1 ns simulation before this, and the water seems to remain in the micelle structure. I'm using a single workstation with Pentium D, 3.0 GHz, and 2Gb of RAM, so I can't manage to get 0.5-1 ns per day.

About the vdwradii.dat that you all said, I'll try to do it. But i'm a beginner in this field (I'm a chemist)..It will take time. By the way, I just thought using Packmol to initially arrange the water to be outside the sphere. So I don't have to use genbox. Can I do that?

Comments and suggestions are greatly appreciated. Thanks a lot.

Alif
 


 
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